Nirav V Malani
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/hiReadsProcessor |
| Branch: RELEASE_3_9 |
| Last Commit: e3a898a |
| Last Changed Date: 2019-05-06 10:01:38 -0400 (Mon, 06 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:05:07 -0400 (Wed, 16 Oct 2019).
| Package 762/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| hiReadsProcessor 1.20.1 Nirav V Malani
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED... | ||||||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| Package: hiReadsProcessor |
| Version: 1.20.1 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings hiReadsProcessor_1.20.1.tar.gz |
| StartedAt: 2019-10-16 02:22:00 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:26:35 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 274.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: hiReadsProcessor.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:hiReadsProcessor.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings hiReadsProcessor_1.20.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/hiReadsProcessor.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘hiReadsProcessor/DESCRIPTION’ ... OK * this is package ‘hiReadsProcessor’ version ‘1.20.1’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘hiReadsProcessor’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE chunkize: no visible global function definition for ‘breakInChunks’ chunkize: no visible global function definition for ‘detectCores’ clusterSites :: no visible binding for global variable ‘queryHits’ clusterSites: no visible binding for global variable ‘clusteredValue’ clusterSites: no visible binding for global variable ‘clusteredValue.freq’ crossOverCheck: no visible binding for global variable ‘queryHits’ decodeByBarcode: no visible global function definition for ‘metadata<-’ decodeByBarcode: no visible global function definition for ‘metadata’ extractSeqs : : no visible global function definition for ‘metadata’ extractSeqs : : : : no visible global function definition for ‘IRanges’ extractSeqs : : : no visible global function definition for ‘IRanges’ findBarcodes: no visible global function definition for ‘metadata<-’ findBarcodes: no visible global function definition for ‘metadata’ findIntegrations: no visible global function definition for ‘fasta.info’ findIntegrations : : no visible global function definition for ‘IRanges’ findVector : : no visible global function definition for ‘IRanges’ pairUpAlignments : : no visible binding for global variable ‘queryHits’ pairwiseAlignSeqs: no visible global function definition for ‘IRangesList’ pairwiseAlignSeqs: no visible global function definition for ‘IRanges’ primerIDAlignSeqs: no visible global function definition for ‘IRanges’ primerIDAlignSeqs: no visible global function definition for ‘IRangesList’ pslToRangedObject: no visible global function definition for ‘IRanges’ read.BAMasPSL: no visible global function definition for ‘ScanBamParam’ read.BAMasPSL: no visible global function definition for ‘scanBamFlag’ read.BAMasPSL: no visible global function definition for ‘DataFrame’ read.SeqFolder: no visible global function definition for ‘SimpleList’ read.psl: no visible global function definition for ‘mclapply’ read.psl : : no visible binding for global variable ‘matches’ read.psl : : no visible binding for global variable ‘misMatches’ read.psl : : no visible binding for global variable ‘qBaseInsert’ read.psl : : no visible binding for global variable ‘tBaseInsert’ read.psl: no visible binding for global variable ‘matches’ read.psl: no visible binding for global variable ‘misMatches’ read.psl: no visible binding for global variable ‘qBaseInsert’ read.psl: no visible binding for global variable ‘tBaseInsert’ read.sampleInfo: no visible global function definition for ‘SimpleList’ splitSeqsToFiles: no visible global function definition for ‘fasta.info’ vpairwiseAlignSeqs: no visible global function definition for ‘Rle’ vpairwiseAlignSeqs: no visible global function definition for ‘runLength’ vpairwiseAlignSeqs: no visible global function definition for ‘IRanges’ vpairwiseAlignSeqs: no visible global function definition for ‘runValue’ Undefined global functions or variables: DataFrame IRanges IRangesList Rle ScanBamParam SimpleList breakInChunks clusteredValue clusteredValue.freq detectCores fasta.info matches mclapply metadata metadata<- misMatches qBaseInsert queryHits runLength runValue scanBamFlag tBaseInsert * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.9-bioc/meat/hiReadsProcessor.Rcheck/00check.log’ for details.
hiReadsProcessor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL hiReadsProcessor ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘hiReadsProcessor’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hiReadsProcessor)
hiReadsProcessor.Rcheck/hiReadsProcessor-Ex.timings
| name | user | system | elapsed | |
| addFeature | 0.307 | 0.024 | 0.330 | |
| addListNameToReads | 0.398 | 0.008 | 0.406 | |
| annotateSites | 0.001 | 0.000 | 0.000 | |
| blatSeqs | 0 | 0 | 0 | |
| chunkize | 0.033 | 0.000 | 0.033 | |
| clusterSites | 0.287 | 0.011 | 0.300 | |
| crossOverCheck | 0.225 | 0.016 | 0.249 | |
| dereplicateReads | 0.041 | 0.000 | 0.042 | |
| doRCtest | 2.451 | 0.504 | 3.166 | |
| extractFeature | 0.241 | 0.082 | 0.229 | |
| extractSeqs | 0.600 | 0.028 | 0.644 | |
| findAndTrimSeq | 1.185 | 0.108 | 1.317 | |
| findBarcodes | 0.786 | 0.000 | 0.788 | |
| findIntegrations | 0 | 0 | 0 | |
| findLTRs | 0 | 0 | 0 | |
| findLinkers | 0 | 0 | 0 | |
| findPrimers | 0 | 0 | 0 | |
| findVector | 0 | 0 | 0 | |
| getIntegrationSites | 1.704 | 0.004 | 1.725 | |
| getSectorsForSamples | 0.136 | 0.003 | 0.139 | |
| getSonicAbund | 0.340 | 0.028 | 0.387 | |
| isuSites | 3.102 | 0.016 | 3.135 | |
| otuSites | 3.679 | 0.012 | 3.734 | |
| pairUpAlignments | 0.000 | 0.000 | 0.001 | |
| pairwiseAlignSeqs | 3.624 | 0.548 | 4.048 | |
| primerIDAlignSeqs | 3.613 | 0.307 | 3.958 | |
| pslCols | 0.001 | 0.001 | 0.001 | |
| pslToRangedObject | 0.215 | 0.003 | 0.220 | |
| read.BAMasPSL | 0 | 0 | 0 | |
| read.SeqFolder | 1.227 | 0.041 | 1.377 | |
| read.blast8 | 0 | 0 | 0 | |
| read.psl | 0 | 0 | 0 | |
| read.sampleInfo | 1.237 | 0.000 | 1.264 | |
| read.seqsFromSector | 0 | 0 | 0 | |
| removeReadsWithNs | 0.024 | 0.000 | 0.025 | |
| replicateReads | 0.031 | 0.000 | 0.031 | |
| sampleSummary | 0.684 | 0.000 | 0.684 | |
| splitByBarcode | 0.037 | 0.000 | 0.046 | |
| splitSeqsToFiles | 0.197 | 0.008 | 0.205 | |
| startgfServer | 0 | 0 | 0 | |
| trimSeqs | 0.028 | 0.000 | 0.028 | |
| vpairwiseAlignSeqs | 3.222 | 0.566 | 3.760 | |
| write.listedDNAStringSet | 0.000 | 0.000 | 0.001 | |
| write.psl | 0.045 | 0.000 | 0.046 | |